Search Results (1,040)

In this study, linear and nonlinear parametric models (M1–M6) were jointly evaluated alongside machine learning (ML)-based approaches to achieve reliable and interpretable prediction of the penetration rate (ROP) of tunnel boring machines (TBMs). The analyses incorporate key geomechanical and structural variables, including the brittleness index (BI), uniaxial compressive strength (UCS), mean spacing of weakness planes (DPW), the angle between the tunnel axis and weakness planes (α), and Brazilian tensile strength (BTS). The coefficients of the parametric models were optimized using the Differential Evolution (DE) algorithm. Variable effects were systematically examined through Jacobian-based elasticity analysis under both original and standardized data scenarios. The results indicate that the M6 model, which explicitly incorporates interaction terms, delivers superior predictive accuracy and a more balanced, physically meaningful representation of variable contributions compared to widely used parametric formulations reported in the literature. While the dominant influence of BI and UCS on ROP is consistently preserved across all models, the indirect contributions of variables such as DPW and BTS are more clearly revealed in M6 owing to its interaction-based structure. Model performance improves systematically with increasing complexity, with the coefficient of determination (R²) rising from 0.62 for M1 to 0.69 for M6. Relative to the linear model, M6 achieves a 9.07% reduction in RMSE and a 10.48% increase in R², while providing additional improvements of 2.47% in RMSE and 2.37% in R² compared with the closest competing model. ML-based variable importance analyses are largely consistent with the parametric findings, highlighting BI and α in tree-based models, and UCS and α in SVM and GAM frameworks. Notably, the GAM exhibits the highest predictive performance under both data scenarios. Overall, the integrated use of parametric and ML approaches establishes a robust hybrid modeling framework that enables highly accurate and engineering-interpretable prediction of TBM penetration rate. Full article

To clarify the phylogenetic relationship between Abutilon theophrasti M. and other Malvaceae plants, the chloroplast genome of A. theophrasti was assembled, annotated, and analyzed. The complete chloroplast genome was sequenced using the Illumina NovaSeq 6000 platform. Bioinformatics methods were employed to systematically analyze its genomic structure, repetitive sequences, nucleic acid diversity, and codon preference. Additionally, a phylogenetic tree was constructed by integrating chloroplast genomic sequences from other Malvaceae species. The results showed that the chloroplast genome of A. theophrasti was 160,440 bp in length with a GC content of 36.89%, exhibiting a typical tetrad structure. A total of 130 coding genes were annotated, including 85 mRNA genes, 37 tRNA genes, and 8 rRNA genes, with no pseudogenes detected. Codon preference analysis indicates that leucine (Leu) is the most frequently used amino acid. There are 31 codons with a relative synonymous codon usage (RSCU) value greater than 1, most of which end with A or U. The genome contains 61 scattered repeat sequences and 288 simple repeat sequences (SSR). Ka/Ks analysis revealed that the overall chloroplast genes of A. theophrasti undergo purifying selection, while genes such as psbK and rps12 are subjected to positive selection, which may be associated with adaptive evolution. Phylogenetically, A. theophrasti is most closely related to its congener A. indicum, followed by a clade comprising M. cathayensis and Malva crispa of the genus Malva. This study enhances the understanding of the phylogenetic relationship of A. theophrasti and provides a theoretical basis for the genetic improvement and breeding strategies of A. theophrasti and other Malvaceae plants. Full article

Population size estimates are essential for investigating numerous aspects of the ecology, evolution, and conservation of wildlife. However, the life cycles of many species include cryptic life stages that are difficult to detect or sample, such as the non-breeding fractions typical of many bird populations. Quantifying the proportions of breeders and non-breeders is crucial to better assess their conservation status and population trends. We propose a simple method applicable to species that show phenotypic differences between adults and juveniles. By quantifying the proportion of ages, the size of the whole population, and its productivity, the size of the non-breeding and breeding fractions can be inferred. We applied this approach to the red-spectacled amazon, Amazona pretrei, a threatened parrot endemic to the Brazilian Atlantic Forest. The entire global population aggregates in winter in a few localities to feed on the seeds of the Parana pine Araucaria angustifolia, a critically endangered tree whose range has declined >97% due to massive exploitation. From a global population of ~16,000 individuals in 2015 and ~20,000 individuals in 2017, our methodology allowed us to estimate a low proportion of juveniles (14%) and a large proportion of non-breeders (80%) within the adult population, with narrow confidence intervals. These proportions did not change between years, but the estimated number of breeding pairs increased, from ca. 1300 to 1700 pairs, in parallel with the global population increase. Our methodology, with its possible improvements to reduce uncertainty in estimates, can be applied to the long-term monitoring of this and many other species, to better understand their conservation challenges and inform effective management strategies. Full article

Sphaerodactylidae play a crucial role in ecosystems, possessing significant ecological, scientific, and conservation value. They contribute to pest control and the maintenance of ecological balance, and also provide abundant materials for research in evolutionary biology and biodiversity. To refine the phylogenetic position of Teratoscincus scincus within the Sphaerodactylidae using mitogenomic data, this study sequenced the complete mitochondrial genome of T. scincus using the Illumina NovaSeq Xplus platform, and subsequently performed assembly, annotation, and analysis. The phylogenetic relationships of T. scincus within the Sphaerodactylidae were analyzed using 13 protein-coding genes (PCGs) from the mitochondrial genome via Bayesian inference (BI) and maximum likelihood (ML) methods. The complete mitochondrial genome of T. scincus is 16,943 bp in length and consists of 13 PCGs, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The base composition shows a distinct AT preference, with the highest A + T content (56.3%) found in the PCGs region. A phylogenetic tree was constructed based on the amino acid sequences of 13 PCGs from the mitochondrial genomes of nine Sphaerodactylidae species retrieved from GenBank and the newly sequenced T. scincus generated in this study. The results confirm that T. scincus belongs to the genus Teratoscincus within the family Sphaerodactylidae. Phylogenetic analysis reveals that T. scincus and Teratoscincus keyserlingii cluster into a monophyletic group, suggesting a close phylogenetic relationship. Additionally, the phylogenetic tree provides new molecular evidence for understanding the formation mechanism of Sphaerodactylidae diversity. This study not only enriches the mitochondrial genome database of Sphaerodactylidae but also lays an important foundation for subsequent research on the adaptive evolution and conservation biology of T. scincus. Full article

Procypris rabaudi, a member of the Cyprinidae family and genus Procypris, has been designated as a national second-class protected wildlife species in China due to a significant decline in its wild populations. Understanding its genomic characteristics and mitochondrial genome structure is crucial for germplasm conservation and systematic classification. In this study, we utilized high-throughput sequencing to investigate the genome of P. rabaudi. The genome size was 1.5 Gb, with a heterozygosity rate of 0.44% and 61.47% of repetitive sequences. We identified 1,151,980 simple sequence repeats (SSRs), with mononucleotide repeats being the most abundant at 55.34%. The complete mitochondrial genome was assembled with 16,595 bp length. A phylogenetic tree constructed from 13 mitochondrial protein-coding genes indicated that genus Procypris was most closely related to genus Luciocyprinus and formed a monophyletic group with Cyprinus, Carassioides, and Carassius. Pairwise Sequentially Markovian Coalescent (PSMC) analysis revealed a rapid population expansion prior to the Last Interglacial Period, followed by a decline after reaching its peak during Last Glacial Period. Notably, P. rabaudi exhibited a two-peak demographic pattern during both the Last Glacial Period. These genomic data provide valuable resources for the conservation of P. rabaudi germplasm and for future studies on cyprinid classification and evolution. Full article

The medicinally and ornamentally valuable genus Thunbergia faces taxonomic uncertainty, while certain Acanthaceae species are threatened by habitat loss, underscoring the need for chloroplast genome studies to support conservation efforts. The chloroplast genome of Thunbergia grandiflora was sequenced and assembled. Additionally, 28 Acanthaceae species with significant medicinal value were selected for comparative genomic analysis. Based on the chloroplast genome data of Acanthaceae species, this study conducted phylogenetic and comparative evolutionary analyses. The results preliminarily support a systematic framework that divides Acanthaceae into eight tribes within five subfamilies. Concurrently, the study revealed significant inverted repeat (IR) region structural variations. A clear correspondence was observed between the contraction of IR length and the topological structure of the phylogenetic tree. In particular, species within the genus Strobilanthes exhibited significant contraction in their IR regions, which corresponded consistently with their tendency to cluster into an independent clade in the phylogenetic tree. This suggests that structural variation in the IR regions may be closely associated with the evolutionary divergence of this group. SSR analysis revealed a prevalent mononucleotide A/T repeat dominant pattern across Acanthaceae species. Furthermore, selection pressure analysis detected positive selection acting on multiple key genes, including rbcL, rps3, rps12, cemA, and ycf4, suggesting that these genes may play important roles in the adaptive evolution of Acanthaceae. This study reveals that the chloroplast genomes of Acanthaceae exhibit distinctive characteristics in phylogenetic architecture, dynamic variations in IR regions, and adaptive evolution of key genes, providing important molecular insights for understanding the mechanisms underlying species diversity and for the conservation of medicinal resources within this family. Full article

Sexual systems critically influence woody plant evolution and forest functioning, yet their global patterns and environmental drivers remain understudied. Investigating the environmental correlates of sexual systems in woody plants is essential for developing targeted conservation and restoration strategies for forest ecosystems. We analyzed sexual system composition of 3595 woody species from 30 ForestGEO forest plots spanning tropical, subtropical, and temperate zones in the Northern Hemisphere. Species were classified by sexual system (hermaphroditism, monoecy, and dioecy) and growth form (trees and shrubs). Community-level patterns were assessed across climatic zones, and the relative contributions of climatic, spatial, and topographic factors were quantified using multivariate and network-based analyses. We observed the following: (1) Sexual system composition exhibited clear climatic differentiation: dioecious species predominate in tropical forests, while monoecious species increased in dominance toward temperate regions. (2) Climatic variables, particularly temperature and precipitation, accounted for more variation in sexual system composition than spatial or topographic factors, although their relative influence differed among climatic zones. (3) Distinct life-form-specific patterns were detected: sexual systems of trees were more strongly associated with broad-scale climatic gradients, whereas those of shrubs were more closely linked to spatial structure and local environmental heterogeneity. Together, these results demonstrate that climate is a dominant but life-form-dependent driver of sexual system biogeography in woody plants, improving trait-based understanding of forest biodiversity responses to climate change. Full article

Forests play a central role in climate change mitigation by acting as biogenic carbon reservoirs and providing renewable biomass for energy systems. In Portugal, where fire-prone landscapes and species composition dynamics pose increasing management challenges, understanding the carbon storage potential of forest biomass is crucial for designing effective decarbonization strategies. This study provides a comprehensive characterization of the Portuguese forest and quantifies the biogenic carbon stored in live and dead biomass across the main forest species. Species-specific carbon contents, rather than the conventional 50% assumption widely used in the literature, were applied to National Forest Inventory data, enabling more realistic and representative carbon stock estimates expressed in kilotonnes of CO₂ equivalent. While the approach relies on inventory-based biomass data and literature-derived carbon fractions and is therefore subject to associated uncertainties, it provides an improved representation of species-level carbon storage at the national scale. Results show that Pinus pinaster, Eucalyptus globulus, and Quercus suber together represent the largest share of carbon storage, with approximately 300,000 kilotonnes of CO₂ equivalent retained in living trees. Wood is the dominant carbon pool, but roots and branches also account for a substantial fraction, emphasizing the need to consider both above- and below-ground biomass in carbon accounting. In parallel, a bibliometric analysis based on the systematic evaluation of scientific publications was conducted to characterize the evolution, thematic focus, and geographic distribution of global research on forest-based biogenic carbon. This analysis reveals a rapidly expanding scientific interest in biogenic carbon, particularly since 2020, reflecting its growing relevance in climate change mitigation frameworks. Overall, the results underscore both the strategic importance of Portuguese forests and the alignment of this research with the broader international scientific agenda on forest-based biogenic carbon. Full article

The epidemiological situation in Poland for IBV GII (formerly known as D1466) has seemed stable over the years, but an increase in such infections has been recently reported. In this study, genetic characterization of the representatives of this genotype was performed in order to determine whether the new epidemic wave of GII IBV was responsible for changes in this status quo. Genotyping based on the complete S1 coding region of eight Polish IBV field strains from 2011 to 2021 confirmed that they belonged to genotype II, with two of them clustered in the two previously identified GII-1 and GII-2 lineages. In turn, the S1 coding region sequences of the next six Polish strains are very different from the previous ones and form a separate group on the phylogenetic tree. However, comprehensive analysis of all complete S1 coding regions of GII strains did not fulfill all parameters needed to create the separate GII lineage, and they all seem to belong to the GII-1 lineage. Further analysis of the partial S1 sequence of 15 IBV GII strains showed their genetic distinctiveness and indicates the ongoing evolution of this virus genotype. Considering the results of our study and the recent outbreaks of GII-2 in Western Europe, it appears that infections with GII virus strains mainly affect egg-producing, long-lived chickens, commercial layers, and breeders. Furthermore, due to the high diversity of these viruses, their circulation in the poultry population may remain undetected, and for this reason, the observed production problems in laying flocks may be attributed to other, unrelated factors. Full article

Nowadays, optimization methods are widely used to adjust controller parameters and tune their optimal values in order to enhance the efficiency and performance of dynamic systems. In this study, the parameters of a linear Proportional–Integral (PI) controller were optimized by using five different optimization algorithms, such as Artificial Tree Algorithm (ATA), Particle Swarm Optimization (PSO), Differential Evolution Algorithm (DEA), Constrained Multi-Objective State Transition Algorithm (CMOSTA), and Adaptive Fire Forest Optimization (AFFO). The optimized controllers were implemented in real time for temperature control of a Heat-flow System (HFS) under various step and time-varying reference signals. In addition, the Ziegler–Nichols (Z–N) method was also applied to the system as a benchmark to compare the temperature tracking performance of the proposed optimization methods. To further evaluate the performance of each optimization algorithm, Mean Absolute Error (MAE) values were calculated, and improvement ratios were obtained. The experimental results showed that the proposed optimization methods provided more successful reference tracking and enhanced controller performance as well. Full article

High-speed silicon (Si) photonic transmitters operating in the O-band require higher on-chip optical power to support advanced modulation formats and ever-increasing line rates. A straightforward approach is to operate laser diodes at higher output power or employ more specialized sources, but this raises cost and exacerbates nonlinear effects such as self-phase modulation, two-photon absorption, and free-carrier generation in high-index-contrast Si waveguides. This paper proposes a low-cost 4 × 1 tree-cascade multimode interference (MMI) power combiner on a Si-on-insulator platform at 1310 nm wavelength that enables coherent power scaling while remaining fully compatible with standard commercial O-band lasers. The device employs adiabatic tapers and low-loss S-bends to ensure uniform field evolution, suppress local field enhancement, and mitigate nonlinear phase accumulation. The optimized layout occupies a compact footprint of 12 µm × 772 µm and achieves a simulated normalized power transmission of 0.975 with an insertion loss of 0.1 dB. Spectral analysis shows a 3 dB bandwidth of 15.8 nm around 1310 nm, across the O-band operating window. Thermal analysis shows that wavelength drift associated with ±50 °C temperature variation remains within the device bandwidth, ensuring stable operation under realistic laser self-heating and environmental changes. Owing to its broadband response, fabrication tolerance, and compatibility with off-the-shelf laser diodes, the proposed combiner is a promising building block for O-band transmitters and photonic neural-network architectures based on cascaded splitter and combiner meshes, while preserving linear transmission and enabling dense, large-scale photonic integration. Full article

Many studies have investigated tree-contact arcing ground faults. However, the effects of branch moisture content and wind speed are still not fully understood. Therefore, this paper addresses the wildfire risk caused by tree-contact arc grounding faults in distribution networks. A 10 kV distribution-line tree-contact arcing fault test platform is built. A two-dimensional multi-physics plasma model is also developed based on magnetohydrodynamics. Experiments and simulations are combined. The effects of wind speed, branch moisture content, and conductor type on arc evolution and fault characteristics are systematically studied. The results show that higher wind speed causes stronger arc-column deformation. The fault current contains more high-frequency components and sharp spikes. At 9 m/s and 16 m/s, the fault current shows strong disturbances and much lower stability. Higher moisture content increases the branch conductivity indirectly. It strengthens the carbonized conductive path and helps sustain stable arcing. For the high-moisture sample (64%), the current waveform is smooth, and its amplitude increases monotonically with fault development. For the low-moisture sample (30%), the current amplitude decreases, and spikes become more frequent. The arc tends to extinguish and reignite repeatedly, which indicates an unstable discharge process. The simulations further reveal the coupling between the arc-root temperature field and the airflow field under different wind speeds and conductivities. They also show clear differences in temperature evolution between bare conductors and insulated conductors. These findings provide experimental evidence and simulation support for identifying wildfires initiated by tree-contact arcing faults. Full article

The self-heating propensity of the fresh wood of ten tree species (two coniferous, eight deciduous) was studied calorimetrically using oxidation heats, q₃₀, at a temperature of 30 °C. Values of q₃₀ in the range between 0.45 W kg⁻¹ (dry) and 1.1 W kg⁻¹ (dry) were found. The lowest evolution of the oxidation heat proved two coniferous wood types—spruce and pine. On the other hand, the highest value of the q₃₀ heat manifested willow wood, which exceeded (as the only one of the samples) the level of 1 W kg⁻¹ (dry). Water was confirmed to promote the generation of oxidation heat, while completely negligible oxidation heat effects were found in dry wood samples. A rise in the heat evolution with increasing moisture content can be explained not only by a change in the mechanistic pathway of the chemical oxidation of wood in the presence of water, but also by the restoration of the activity of microorganisms in wood, which occurs only at a sufficient level of moisture content. Tree bark appears to be probable carrier of a diverse microbiome. Based on the experiments with debarked wood samples, it can be estimated that the part of the heat produced by microorganisms constitutes a remarkable 35–55% of the global oxidation heat q₃₀, as determined for fresh wood samples. Full article

Dam break problem-induced floods can trigger hazardous dike overtopping, demanding predictions that are fast, accurate, and interpretable. We pursue two objectives: (i) introducing a new alpha evolution (AE) optimization scheme to improve tree-model predictive accuracy, and (ii) developing a cluster-wise modeling strategy in which regimes are defined by wave characteristics. Using a dataset generated via physical model experiments and smoothed particle hydrodynamics (SPH) numerical simulations, we first group samples via hierarchical clustering (HC) on the Froude number $\left(\mathrm{Fr}\right)$, wave nonlinearity $\left(R\right)$, and relative distance to the dike $\left(D\right)$. We then benchmark CatBoost, XGBoost, and ExtraTrees within each cluster and select the best-performing CatBoost as the baseline, after which we train standard CatBoost and its AE-optimized variant. Under random train–test splits, AE-CatBoost achieves the strongest generalization for predicting relative run-up distance $H_m$ (testing dataset $R^2=0.9803$, $\mathrm{RMSE}=0.0599$), outperforming particle swarm optimization (PSO) and grid search (GS)-tuned CatBoost. We further perform TreeSHAP analyses on AE-CatBoost for global, local, and interaction attributions. SHAP analysis yields physics-consistent explanations: D dominates, followed by H and L, with a weaker positive effect of $\mathrm{Fr}$ and minimal influence of R; $H\times D$ is the strongest interaction pair. Overall, AE optimization combined with HC-based cluster-wise modeling produces accurate, interpretable overtopping predictions and provides a practical route toward field deployment. Full article

Okra (Abelmoschus esculentus L. Moench) is an annual herbaceous plant belonging to the Malvaceae family. Its medicinal properties and edible value have attracted widespread scientific attention, yet its systematic taxonomy, evolution, and photosynthetic mechanisms warrant further investigation. Chloroplasts, specialized semi-autonomous organelles within green plants, possess their own genetic material and serve as an excellent source of genetic information. This study employed Illumina high-throughput sequencing technology to sequence the complete chloroplast genome of the cultivar ‘Gan Kui No. 1’. The complete chloroplast genome was determined to be 163,121 bp in length, with A, C, G, T, and GC nucleotides accounting for 31.24%, 18.71%, 18.02%, 32.02%, and 36.74% of the total, respectively. It exhibits a classic tetrad structure, comprising one large single-copy region (88,071 bp), one small single-copy region (19,032 bp), and one pair of inverted repeat regions (28,009 bp). The entire chloroplast genome contains 132 annotated genes, including 37 tRNA genes, 8 rRNA genes, 87 mRNA genes, and 0 pseudogenes. A phylogenetic tree constructed using 20 species, including Abelmoschus esculentus, revealed a clear phylogenetic relationship between the genus Hibiscus and Abelmoschus esculentus. The complete gene sequences have been uploaded to the NCBI database (accession number PX590535). This study provides insights into understanding the evolutionary relationships of Abelmoschus esculentus and refining its taxonomy, laying a theoretical foundation for subsequent research on the Abelmoschus esculentus chloroplast genome. Full article